Capturing cell-type-specific activities of cis-regulatory elements from peak-based single-cell ATAC-seq dlvr.it/TJLSkx

🎉bioRxiv & medRxiv are now managed by openRxiv, a new independent nonprofit. This transition allows for more flexibility and innovation. Our community-centered mission remains being a free service to authors ensuring rapid sharing of scientific information before peer review. 🧵

My paper on profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag is officially out at Molecular Cell. Check it out! cell.com/molecular-cell…

🧬 Researchers at Fred Hutch Cancer Center have uncovered an overlooked mechanism driving aggressive breast and brain tumors. Learn more about the 64 ancestral genes investigated by the Henikoff lab: bit.ly/3XIke4Y Science Magazine abstract: bit.ly/4iGJAbtResearc…

Excited to share another collaborative study with Dr. Joe Costello - Intratumor heterogeneity of 3D genome organization in primary glioblastoma samples. Led by Qixuan and Juan, and congrats to the whole team! Lurie Cancer Center Northwestern Feinberg School of Medicine UCSF Neurosurgery science.org/doi/10.1126/sc…

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/longc…

1/10 Excited to share our latest - the first whole-body map of both DNA methylation and 3D genome at single-cell resolution.

Proseg is a segmentation tool for single-cell spatial transcriptomics data that uses unsupervised probabilistic modeling of transcript spatial distribution, for accurate segmentation without multimodal staining. nature.com/articles/s4159…

Our spatial FFPE-ATAC-seq is now published in Nature Communications! With extensive optimizations, it performs well across diverse tissues, unlocking the vast FFPE archive for spatial epigenomics. Big congrats to Pengfei Guo Pengfei_Guo, Yufan Chen, and the team! nature.com/articles/s4146…

📢 Now live at ⁦nature⁩ Our team discovered that PPP2R1A mutations are linked to improved response to immunotherapy in ovarian clear cell carcinoma. ⁦Yibo⁩ ⁦Amir Jazaeri⁩ ⁦Rugang Zhang Lab⁩ ⁦⁦MD Anderson Cancer Center⁩ nature.com/articles/s4158…

Our scMicro-C paper is out in Nature Genetics! Huge thanks to the reviewers for their valuable insights, to SunneyXie for unwavering support, and to fantastic collaborators Jiankun Zhang & Longzhi Tan. Thrilled to share this work!

Introducing TCAT, a pipeline to simultaneously capture gene expression programs related to T cell subsets and activation states. nature.com/articles/s4159…

Excited to share our new paper in Nature Methods! 🚀 We present iSCALE, a “Google Map” for spatial transcriptomics, scaling cellular-resolution gene expression mapping to large-sized tissues beyond the reach of current platforms. 👉nature.com/articles/s4159…

GHIST: a deep learning-based method to predict spatial gene expression at high resolution using histology data. nature.com/articles/s4159…

It was a pleasure to write this piece in Nature Methods on GHIST & iSCALE. These two methods transform H&E histology into molecular maps, predicting gene expression at single-cell and whole-slide resolution, expanding spatial omics at scale!

[1/10] We’re excited to introduce CytoTRACE 2 — a major upgrade for inferring developmental potential from single-cell RNA-seq across datasets. Nature Methods Led by Minji Kang in Aaron Newman Lab. 📄 Paper: nature.com/articles/s4159… 🔗 Shareable link: rdcu.be/eMTVO

Thrilled see our paper out in nature ! 🤩 Wonderful collaboration with GonçaloCasteloBranco. Kudos to my amazing postdoc Di at Yale Engineering and Leslie Kirby from Goncalo's lab Karolinska Institutet. Huge team science with Yale School of Medicine UC San Francisco A*STAR nature.com/articles/s4158…